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The ORR said that Network Rail (NR) had fallen short of its target of running 92 per cent of long-distance trains on time by 2013/14.

There was "deteriorating performance on key parts of the rail network in England and Wales".

ORR chief executive Richard Price said: "Passengers need to be able to rely on the railways to get them from A to B throughout the whole year. However, NR's operational performance on parts of Britain's rail network has been poor over recent months.”

Top NR directors can earn one-year and three-year performance bonuses possibly running into hundreds of thousands of pounds.

NR chief executive Sir David Higgin's salary as at March 31 2012 was £560,000, with finance director Patrick Butcher on £382,000 and operations and customer services director Robin Gisby on £360,000.

Sir David accepted it had been a “difficult period” for passengers but added: “The damage that extreme weather can do to a Victorian rail network which was neither designed nor built for such challenges is clear.

“Whole lines were closed by flooding and tracks came close to being washed away by rivers which burst their banks.

“On the worst-affected parts of the network, torrential rain caused up to 60 landslides in a single day.

"This has been a wake-up call for the whole industry, which we ignore at our peril.”

But Manuel Cortes, leader of the TSSA rail union, said: "Blaming the Victorian railway for poor performance is a bit like a child claiming the dog ate his homework. NR has consistently failed to hit punctuality targets, regardless of bad weather.

"We trust that in the light of these latest poor figures, NR bosses will now cancel their own plans to double their already-large salaries with new annual and long-term bonuses."

Shadow transport secretary Maria Eagle said: "In light of today's report and the poor performance highlighted, NR bosses should show passengers good faith and rule out taking any bonuses this year."